Evaluate gene sets by cell type-specific gene expression

Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(stringr)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name

## [1] "Micro-PVM"

graph_weight

## [1] "0.5"

Check the expression of each gene set in each brain-related cell type

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

length(assayed_genes)

## [1] 2000

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)

##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    7.00   22.00   26.00   24.57   28.25   30.00

length(n_genes)

## [1] 40

sort(n_genes)

##  [1]  7 14 15 17 19 21 21 21 21 22 22 23 23 23 24 25 25 26 26 26 26 26 26 26 27
## [26] 27 27 28 28 28 29 29 29 29 29 29 29 30 30 30

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

table(is.na(a2s))

## 
## FALSE  TRUE 
##  1739   261

table(a2s == assayed_genes, useNA = 'ifany')

## 
## FALSE  TRUE  <NA> 
##    21  1718   261

gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]

##     sym_in_data   sym_limma
##  1:       LRRC6     DNAAF11
##  2:    C11orf49      CSTPP1
##  3:   LINC00476 ERCC6L2-AS1
##  4:  HNRNPA1P48   HNRNPA1L3
##  5:  ZRANB2-AS2   ZRANB2-DT
##  6:   LINC00271     AHI1-DT
##  7:    RFX3-AS1     RFX3-DT
##  8:   LINC00884  ATP13A3-DT
##  9:   FBXO30-DT    EPM2A-DT
## 10:   LINC00894    EOLA2-DT
## 11:   COX10-AS1    COX10-DT
## 12:   LINC01184  SLC12A2-DT
## 13: FAM198B-AS1  GASK1B-AS1
## 14:     C5orf17   LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16:   LINC01146       HISLA
## 17:      BTBD11       ABTB3
## 18:       H2BU1      H2BC26
## 19:      SKIV2L       SKIC2
## 20:     FAM155A       NALF1
## 21:  CTB-41I6.2   PIK3R5-DT
##     sym_in_data   sym_limma

gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)

## [1] 2000    3

gene_info[1:5,]

##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
## 3:        PDK4      PDK4        PDK4
## 4:       CALCR     CALCR       CALCR
## 5:       ABCB4     ABCB4       ABCB4

t1 = table(gene_info$gene_symbol)
table(t1)

## t1
##    1 
## 2000

Read in cell type-specific expression data

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

ct = fread("../Annotation/rna_single_cell_type.tsv.gz")
dim(ct)

## [1] 1587110       4

ct[1:5,]

##               Gene Gene name             Cell type  nTPM
## 1: ENSG00000000003    TSPAN6            Adipocytes 149.5
## 2: ENSG00000000003    TSPAN6 Alveolar cells type 1   6.1
## 3: ENSG00000000003    TSPAN6 Alveolar cells type 2  10.5
## 4: ENSG00000000003    TSPAN6            Astrocytes  13.9
## 5: ENSG00000000003    TSPAN6               B-cells   1.5

length(unique(ct$`Cell type`))

## [1] 79

table(ct$`Cell type`)

## 
##                      Adipocytes           Alveolar cells type 1 
##                           20090                           20090 
##           Alveolar cells type 2                      Astrocytes 
##                           20090                           20090 
##                         B-cells             Basal keratinocytes 
##                           20090                           20090 
##           Basal prostatic cells         Basal respiratory cells 
##                           20090                           20090 
## Basal squamous epithelial cells                   Bipolar cells 
##                           20090                           20090 
##          Breast glandular cells      Breast myoepithelial cells 
##                           20090                           20090 
##                  Cardiomyocytes                  Cholangiocytes 
##                           20090                           20090 
##                      Club cells           Collecting duct cells 
##                           20090                           20090 
##        Cone photoreceptor cells                Cytotrophoblasts 
##                           20090                           20090 
##                 dendritic cells              Distal enterocytes 
##                           20090                           20090 
##            Distal tubular cells                    Ductal cells 
##                           20090                           20090 
##                Early spermatids      Endometrial ciliated cells 
##                           20090                           20090 
##       Endometrial stromal cells               Endothelial cells 
##                           20090                           20090 
##           Enteroendocrine cells                 Erythroid cells 
##                           20090                           20090 
##              Excitatory neurons        Exocrine glandular cells 
##                           20090                           20090 
##       Extravillous trophoblasts                     Fibroblasts 
##                           20090                           20090 
##   Gastric mucus-secreting cells     Glandular and luminal cells 
##                           20090                           20090 
##                    granulocytes                 Granulosa cells 
##                           20090                           20090 
##                     Hepatocytes                  Hofbauer cells 
##                           20090                           20090 
##                Horizontal cells              Inhibitory neurons 
##                           20090                           20090 
##         Intestinal goblet cells                       Ionocytes 
##                           20090                           20090 
##                   Kupffer cells                Langerhans cells 
##                           20090                           20090 
##                 Late spermatids                    Leydig cells 
##                           20090                           20090 
##                     Macrophages                     Melanocytes 
##                           20090                           20090 
##                Microglial cells                       monocytes 
##                           20090                           20090 
##           Mucus glandular cells               Muller glia cells 
##                           20090                           20090 
##                        NK-cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes      Pancreatic endocrine cells 
##                           20090                           20090 
##                    Paneth cells               Peritubular cells 
##                           20090                           20090 
##                    Plasma cells       Prostatic glandular cells 
##                           20090                           20090 
##            Proximal enterocytes          Proximal tubular cells 
##                           20090                           20090 
##      Respiratory ciliated cells         Rod photoreceptor cells 
##                           20090                           20090 
##             Salivary duct cells                   Schwann cells 
##                           20090                           20090 
##          Serous glandular cells                   Sertoli cells 
##                           20090                           20090 
##               Skeletal myocytes             Smooth muscle cells 
##                           20090                           20090 
##                   Spermatocytes                   Spermatogonia 
##                           20090                           20090 
##       Squamous epithelial cells        Suprabasal keratinocytes 
##                           20090                           20090 
##            Syncytiotrophoblasts                         T-cells 
##                           20090                           20090 
##                     Theca cells         Thymic epithelial cells 
##                           20090                           20090 
##          Undifferentiated cells 
##                           20090

cell_group = fread("../Annotation/rna_single_cell_type_brain.tsv")
dim(cell_group)

## [1] 16  2

cell_group[1:2,]

##             Cell_type Cell_group
## 1: Excitatory neurons   Neuronal
## 2: Inhibitory neurons   Neuronal

ct = ct[`Cell type` %in% cell_group$Cell_type,]
table(ct$`Cell type`)

## 
##                      Astrocytes                         B-cells 
##                           20090                           20090 
##                   Bipolar cells        Cone photoreceptor cells 
##                           20090                           20090 
##              Excitatory neurons                Horizontal cells 
##                           20090                           20090 
##              Inhibitory neurons                Microglial cells 
##                           20090                           20090 
##               Muller glia cells Oligodendrocyte precursor cells 
##                           20090                           20090 
##                Oligodendrocytes                    Plasma cells 
##                           20090                           20090 
##         Rod photoreceptor cells                   Schwann cells 
##                           20090                           20090 
##                         T-cells 
##                           20090

Check gene expression for each gene set

dim(gene_info)

## [1] 2000    3

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]

  n_genes = sum(genes %in% ct$`Gene name`)
  print(sprintf("found %d genes.", n_genes))

  if(n_genes == 0) { next }

  df = ct[`Gene name` %in% genes,]
  dim(df)
  df[1:2,]
  
  stopifnot(all(str_to_lower(df$`Cell type`) %in% 
                  str_to_lower(cell_group$Cell_type)))
  
  mat1 = match(str_to_lower(df$`Cell type`), 
               str_to_lower(cell_group$Cell_type))
  
  df = cbind(df, cell_group[mat1,])
  df[1:2,]
  
  df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
  df$Cell_group = factor(df$Cell_group, 
                         levels = unique(cell_group$Cell_group))
  
  p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) + 
    geom_boxplot() + xlab("Cell type") + ggtitle(set_k) + 
    theme(axis.text.x = element_text(angle = 45, hjust = 1)) + 
    scale_fill_brewer(palette="RdBu")

  print(p1)
}

## [1] 1
##  [1] "MCTP2"         "ADAMTS3"       "GHRL"          "HESX1"        
##  [5] "UCN"           "WDR25"         "EYS"           "PAPSS2"       
##  [9] "CARNMT1-AS1"   "MTCP1"         "LINC01277"     "LINC00271"    
## [13] "LINC02884"     "RPL34-DT"      "RP11-195C7.1"  "KCNMA1-AS1"   
## [17] "RP11-544A12.8" "STARD4-AS1"    "C5orf17"       "LINC02196"    
## [21] "MIR100HG"      "RP1-71H24.1"   "LINC02444"     "RP11-58G13.1" 
## [25] "RP11-354K4.2"  "TRG-AS1"       "RP11-237N2.1"  "RP11-314E10.1"
## [1] "found 9 genes."

## [1] 2
##  [1] "MTERF1"        "PIGC"          "ADAMTS19"      "ADGRG5"       
##  [5] "BEX3"          "FLJ40194"      "TMEM151B"      "PCED1B"       
##  [9] "H2BC4"         "H2BC18"        "COL5A2"        "ENTPD3-AS1"   
## [13] "TEX41"         "ZNF451-AS1"    "RP4-568F9.6"   "RP11-557H15.4"
## [17] "LINC02642"     "BDNF-AS"       "LINC02057"     "AC008697.1"   
## [21] "CTD-2537O9.1"  "RP11-370I10.6" "H2AC19"        "H2BC8"        
## [25] "H2AC8"         "RP11-495L19.1" "RP11-321P16.3" "RP11-399K19.1"
## [1] "found 13 genes."

## [1] 3
##  [1] "SIGLEC1"       "ADGRD1"        "F13A1"         "CH25H"        
##  [5] "TMEM44"        "BANK1"         "ADAMTS15"      "ODF3B"        
##  [9] "RP11-445F6.2"  "LINC01515"     "AC002539.1"    "RP3-525N10.2" 
## [13] "AC007682.1"    "RP11-142A5.1"  "LINC02211"     "FAM66D"       
## [17] "OVCH1-AS1"     "CTD-2336H13.2" "LINC02073"     "CERNA2"       
## [21] "LINC02885"     "RP11-38B6.1"  
## [1] "found 8 genes."

## [1] 4
##  [1] "APBB1IP"   "ACER3"     "PLEK"      "TBC1D14"   "NPL"       "ARMH4"    
##  [7] "GAREM1"    "RASGEF1C"  "AOPEP"     "DISP1"     "DEPTOR"    "ATF7IP2"  
## [13] "MARCHF3"   "DLEU1"     "SLC8A1"    "SCFD2"     "PRKN"      "MBD5"     
## [19] "HMGA1P4"   "XACT"      "LINC01094" "RNASET2"   "ARHGAP6"   "PADI2"    
## [25] "FMN1"     
## [1] "found 21 genes."

## [1] 5
##  [1] "CELSR3"        "GALNT16"       "LILRB5"        "HS3ST2"       
##  [5] "NRG2"          "JAML"          "PLPP3"         "RANBP3L"      
##  [9] "FSTL5"         "STXBP6"        "HPSE2"         "LRRC3B"       
## [13] "ADGRB1"        "VMO1"          "POTEG"         "ZNF521"       
## [17] "FAM153CP"      "FAM229A"       "RP11-47I22.3"  "AF064858.8"   
## [21] "TRHDE-AS1"     "AC002066.1"    "RP11-696N14.1" "CPEB2-DT"     
## [25] "SELENOP"       "RP11-79E3.2"   "RP11-661A12.5" "RP11-429A20.3"
## [29] "RP11-396B14.2" "RP11-436D23.1"
## [1] "found 18 genes."

## [1] 6
##  [1] "MMP24"         "C4orf19"       "CYTL1"         "ENO4"         
##  [5] "FAM177B"       "CLEC9A"        "INSYN2B"       "ANKUB1"       
##  [9] "ELMO1-AS1"     "TMLHE-AS1"     "ENTPD1-AS1"    "AC096558.1"   
## [13] "SRGAP2-AS1"    "AC037445.1"    "RP11-528G1.2"  "DIAPH2-AS1"   
## [17] "LINC01141"     "MEF2C-AS2"     "LINC02742"     "RP11-649G15.2"
## [21] "RP11-452H21.1" "CTD-2647E9.3"  "RP11-815J21.4" "ABHD15-AS1"   
## [25] "RP11-16C1.3"   "RP11-793A3.2"  "CTD-3149D2.4"  "CTD-2282P23.2"
## [29] "DISC2"        
## [1] "found 8 genes."

## [1] 7
##  [1] "NAV3"        "LY96"        "FGGY"        "ZDHHC14"     "KCNQ3"      
##  [6] "MIR99AHG"    "MEF2C-AS1"   "LINC02232"   "ATP6V0D1-DT" "KCNQ2"      
## [11] "CUX2"        "FRMD4B"      "WDR45B"      "SLC2A5"      "HSPA12A"    
## [16] "RBFOX3"      "MYO1D"       "KCNQ5"       "ZNF846"      "ZNF407"     
## [21] "LNCAROD"    
## [1] "found 16 genes."

## [1] 8
##  [1] "TENT5A"        "CYREN"         "TMEM241"       "RALGPS1"      
##  [5] "SLC49A4"       "GASK1A"        "PUS10"         "GASK1B"       
##  [9] "ACYP2"         "RNLS"          "LIPE-AS1"      "ALOX12-AS1"   
## [13] "HDAC2-AS2"     "COX10-AS1"     "MIR4300HG"     "RP11-10H3.1"  
## [17] "C8orf37-AS1"   "RP11-554D14.6" "LINC02328"     "RP11-187O7.3" 
## [21] "MIR222HG"      "RP11-323F24.5" "RP1-111C20.3"  "RP11-574F11.4"
## [25] "ATOH8"         "KLF13"        
## [1] "found 12 genes."

## [1] 9
##  [1] "IFT43"   "ATP5F1E" "STAB1"   "LCP2"    "HDHD5"   "SESN1"   "DOCK3"  
##  [8] "BICRAL"  "GTDC1"   "AFDN"    "PRAM1"   "CCDC40"  "NR6A1"   "RSU1"   
## [15] "SLC2A13" "SH3RF1"  "ST3GAL2" "NEK10"   "PRKG1"   "AIDA"    "GLDN"   
## [22] "PARVB"   "IARS1"  
## [1] "found 23 genes."

## [1] 10
##  [1] "SNCAIP"    "PITPNM2"   "PROCR"     "IL1A"      "C3"        "FGF13"    
##  [7] "STON2"     "RNF157"    "KCNMB1"    "KCNMA1"    "TSPAN7"    "TAGAP"    
## [13] "RIC3"      "P2RY12"    "XIST"      "LINC01091" "MMP28"     "RGCC"     
## [19] "SH3BP5"    "LPL"       "KCNE1"    
## [1] "found 19 genes."

## [1] 12
##  [1] "OPHN1"        "CASS4"        "RIPOR2"       "PDE10A"       "PLCL1"       
##  [6] "AHI1"         "WDPCP"        "UNC80"        "IRAK1BP1"     "TENM4"       
## [11] "CACNA1D"      "SMIM14"       "ZNF608"       "CAPS2"        "FIGN"        
## [16] "RTN4RL1"      "COL25A1"      "PRDX6-AS1"    "AC011288.2"   "LINC00894"   
## [21] "GMDS-DT"      "RP11-673E1.1" "RP11-160E2.6" "RP4-681L3.3"  "HIVEP2"      
## [26] "MCTP1"       
## [1] "found 19 genes."

## [1] 13
##  [1] "SLC1A3"   "RAPGEF1"  "PTPRE"    "SSH2"     "FER"      "MGAT5"   
##  [7] "FMNL2"    "CDC42SE2" "RUNX1"    "CLASP2"   "OXR1"     "LDLRAD4" 
## [13] "GPHN"     "BNC2"     "CHD2"     "PACS1"    "PCDH9"    "PDE4B"   
## [19] "NEAT1"   
## [1] "found 18 genes."

## [1] 14
##  [1] "NIPAL2"        "CPED1"         "GPAT3"         "SESN3"        
##  [5] "ARHGAP42"      "CYSLTR1"       "RAB39A"        "CATSPERE"     
##  [9] "CDIN1"         "SDHAF3"        "MAMDC2-AS1"    "FIRRE"        
## [13] "CTA-292E10.6"  "RP11-37B2.1"   "RP11-630C16.2" "RP11-946L16.1"
## [17] "MIR223HG"      "SNX25"         "OGFRL1"        "SEM1"         
## [21] "RASGEF1B"      "C17orf67"      "CLEC5A"       
## [1] "found 16 genes."

## [1] 15
##  [1] "SLC5A9"        "RAB38"         "CFAP74"        "TCERG1L"      
##  [5] "SPDYE2"        "RP11-165F24.3" "RP11-526K17.2" "HCG22"        
##  [9] "LINC00960"     "RP11-712B9.2"  "RP11-381K20.2" "RP11-39E3.3"  
## [13] "RP11-434H14.1" "RP11-493L12.3" "RP11-317G6.1"  "PRKCA-AS1"    
## [17] "H2BC7"         "RP11-622O11.6" "COL5A3"        "SLC26A7"      
## [21] "SNED1"         "HTR1E"         "DIRC3"         "DARS1-AS1"    
## [25] "CYP1B1-AS1"    "AC092835.2"    "MIR155HG"      "RP11-384C4.7" 
## [29] "LINC01138"    
## [1] "found 10 genes."

## [1] 16
##  [1] "SYNDIG1"       "FAM149A"       "SPATA6"        "C1QC"         
##  [5] "MIR31HG"       "LINC01357"     "FTCDNL1"       "RP11-162D16.2"
##  [9] "RP11-120D5.1"  "LINC01684"     "CEACAM16-AS1"  "LINC00907"    
## [13] "KCNQ1OT1"      "RP11-74J13.8"  "EIF1B-AS1"     "RP11-437L7.2" 
## [17] "RP11-685G11.1" "APBB3"         "DARS1"         "COL5A1"       
## [21] "MFSD4B"        "H2AC6"         "ZC3H6"         "CTD-2643I7.5" 
## [25] "RP11-707P17.1" "RP11-452F19.4"
## [1] "found 11 genes."

## [1] 17
##  [1] "ZNF532"                    "ARHGEF18"                 
##  [3] "PLAGL1"                    "FLVCR2"                   
##  [5] "PUDP"                      "PCBD2"                    
##  [7] "ARHGAP20"                  "SAMSN1"                   
##  [9] "DENND2B"                   "CDYL2"                    
## [11] "SPTLC3"                    "MICOS10"                  
## [13] "PGBD5"                     "B3GLCT"                   
## [15] "TMSB4X"                    "LINC00630"                
## [17] "RP11-535M15.1"             "SLC16A1-AS1"              
## [19] "LMCD1-AS1"                 "PVT1"                     
## [21] "LIX1-AS1"                  "LINC01605_ENSG00000253161"
## [23] "RP11-588H23.3"             "LINC01146"                
## [25] "RP11-281A20.2"             "RP11-692P14.1"            
## [27] "RP11-111G13.1"            
## [1] "found 15 genes."

## [1] 18
##  [1] "PRKCQ"    "PKD2L2"   "ANGPT2"   "MAP2K6"   "NEK11"    "PTPRB"   
##  [7] "FMO5"     "PDE5A"    "EFCAB11"  "MED12L"   "MTHFD2L"  "TMEM52B" 
## [13] "SLC35G2"  "KCNMB2"   "LTC4S"    "KIF9-AS1" "CNTN1"    "HGF"     
## [19] "RASGRP2"  "EMILIN2"  "CRIM1"    "CAMK4"    "KCND3"    "C11orf80"
## [25] "PPM1E"    "NELL2"   
## [1] "found 25 genes."

## [1] 19
##  [1] "LRRC7"        "ARHGAP10"     "RAPGEF4"      "FGF14"        "ADAM23"      
##  [6] "ATP8A2"       "PDZD2"        "STXBP5L"      "PAM"          "TENM2"       
## [11] "ADGRL3"       "NCAM2"        "CSMD3"        "NLGN1"        "CTNND2"      
## [16] "FUT9"         "CADM2"        "RIMS2"        "NRXN1"        "FLRT2"       
## [21] "NRG3"         "TAFA2"        "LINC00632"    "SNHG14"       "RP11-384F7.2"
## [26] "IQCJ-SCHIP1" 
## [1] "found 23 genes."

## [1] 20
##  [1] "SGCE"           "C11orf65"       "RP11-321C24.1"  "ARHGAP26-AS1"  
##  [5] "ALG13-AS1"      "RP11-353M9.1"   "MYCBP2-AS1"     "CCDC200"       
##  [9] "AC018890.6"     "ZBTB20-AS5"     "CTD-2015H6.3"   "RP11-268P4.5"  
## [13] "CTD-3239E11.2"  "RP11-238K6.1"   "RP11-513G19.1"  "RP11-571M6.7"  
## [17] "RP11-136F16.1"  "RP11-713N11.4"  "USP3-AS1"       "RP11-16B9.1"   
## [21] "RP11-106M3.3"   "RNF213-AS1"     "RP11-737O24.2"  "RP11-53B2.3"   
## [25] "RP4-769N13.7"   "RP11-793H13.14" "RP11-458A7.1"   "RP11-1146N6.3" 
## [29] "RP11-685G9.5"   "CTD-2021K4.2"  
## [1] "found 3 genes."

## [1] 21
##  [1] "PER3"      "CYFIP2"    "DHRS9"     "RPS6KA5"   "STMN2"     "ABCG2"    
##  [7] "SLC22A23"  "PTPN14"    "CCDC171"   "PLEKHA7"   "GAP43"     "SVIL"     
## [13] "LINC01278" "FOSL2"     "SLC16A10"  "CYTIP"     "HIP1"      "PARP8"    
## [19] "SRSF12"    "AGAP1"     "FAM110B"   "ZFPM2"    
## [1] "found 21 genes."

## [1] 22
##  [1] "ANGPTL1"       "ITGA9"         "AGBL3"         "LINC00539"    
##  [5] "AC017101.10"   "RP1-225E12.2"  "COA6-AS1"      "AC083884.8"   
##  [9] "RP11-666F17.1" "DENND6A-AS1"   "RP11-692D12.1" "RP11-679C8.2" 
## [13] "RP11-703M24.5" "RP11-7F3.1"    "AC009166.9"    "ZFY"          
## [17] "PXDNL"         "RNF150"        "LINC00910"     "H1-0"         
## [21] "KLF3-AS1"      "LINC02646"     "RP11-351A11.1" "HIF1A-AS3"    
## [25] "RP11-322M13.1" "CTD-2285E13.1" "RP11-404C6.6" 
## [1] "found 7 genes."

## [1] 23
##  [1] "NEURL2"                  "LILRB2"                 
##  [3] "PEBP4"                   "IGSF11"                 
##  [5] "ADGRA3"                  "LINC00467"              
##  [7] "SLC9B1"                  "H2AC20"                 
##  [9] "FSIP2"                   "LINC01285"              
## [11] "ATP6AP1L"                "AC003090.1"             
## [13] "RMDN2-AS1"               "LINC01376"              
## [15] "MEIKIN"                  "RP11-246A10.1"          
## [17] "ALG1L9P_ENSG00000248671" "AC006160.5"             
## [19] "RP11-1H15.2"             "RP11-511B23.2"          
## [21] "RP11-638I2.8"            "LINC00639"              
## [23] "RP11-221G19.1"           "RP1-18C9.3"             
## [25] "RP11-21M24.6"            "RP11-65F13.4"           
## [27] "RP11-56I23.2"            "AMER2"                  
## [29] "LINC00970"              
## [1] "found 10 genes."

## [1] 24
##  [1] "LINC00996"               "SLC26A3"                
##  [3] "HELLS"                   "CHI3L1"                 
##  [5] "LYPD5"                   "TNFRSF11B"              
##  [7] "LINC02397"               "ARL17B"                 
##  [9] "MYO16-AS1"               "RP3-467L1.4"            
## [11] "RP11-657O9.1"            "RP11-13N12.1"           
## [13] "MTRNR2L1"                "RP11-81K2.1"            
## [15] "SCARNA2_ENSG00000270066" "LINC00551"              
## [17] "CH507-513H4.1"          
## [1] "found 7 genes."

## [1] 25
##  [1] "PCSK1N"         "IER3"           "ARL5C"          "AZIN2"         
##  [5] "NLGN4Y"         "MIR4435-2HG"    "GLIPR1L1"       "TMEM72-AS1"    
##  [9] "RP1-30E17.2"    "SLC8A1-AS1"     "MIR646HG"       "KCNMB2-AS1"    
## [13] "ARHGAP8"        "STX18-AS1"      "ANK2-AS1"       "RP11-281P23.2" 
## [17] "ZFPM2-AS1"      "MAILR"          "AP000487.6"     "RP11-516C1.1"  
## [21] "LINC00621"      "RP11-399K21.11" "LINC02712"      "RP11-305E17.8" 
## [25] "RP11-19D22.1"   "RP11-264E23.4"  "RP11-555K12.4"  "PCDH11Y"       
## [1] "found 8 genes."

## [1] 26
##  [1] "PEX7"          "RAB40B"        "ARAP2"         "ABCA7"        
##  [5] "FAM107B"       "SLC9A7"        "RNMT"          "IL4I1"        
##  [9] "DCUN1D4"       "ZC4H2"         "BTG1"          "ADCY3"        
## [13] "FAM117B"       "COLEC12"       "CCDC107"       "FRMD5"        
## [17] "RBM44"         "ARL4C"         "SYCP2"         "H2BU1"        
## [21] "CR1L"          "CD247"         "DENND1B"       "AS3MT"        
## [25] "USP2-AS1"      "RP11-368L12.1"
## [1] "found 23 genes."

## [1] 27
##  [1] "P3H2"       "AKAP7"      "ACVR2A"     "PLAU"       "SMAD6"     
##  [6] "CCDC102B"   "PRMT9"      "SLC9A9"     "KCNIP1"     "DYNC2H1"   
## [11] "HLA-DRA"    "CYTH1"      "AGAP3"      "CSGALNACT1" "EVA1C"     
## [1] "found 15 genes."

## [1] 28
##  [1] "RPL3"       "RPL18A"     "RPL19"      "RPL34"      "RPL24"     
##  [6] "LDAH"       "RPS24"      "RPS2"       "RPS11"      "RPL11"     
## [11] "RPS27A"     "RPL32"      "RAB28"      "RPL26"      "RPL38"     
## [16] "RPLP2"      "RPS23"      "RPL12"      "RPL23A"     "ZNF433-AS1"
## [21] "ADARB1"    
## [1] "found 20 genes."

## [1] 29
##  [1] "MAP3K20"       "ARRDC2"        "CDH26"         "KIAA0513"     
##  [5] "CCNG2"         "PGGHG"         "TIAM2"         "AMN1"         
##  [9] "CFAP161"       "ANKRD30BL"     "MARCHF8"       "PDZRN4"       
## [13] "CXXC5"         "LINC00862"     "RP5-864K19.4"  "SGO1-AS1"     
## [17] "RP11-147G16.1" "RP11-154D17.1" "RP11-305L7.3"  "SLC5A4-AS1"   
## [21] "LINC01322"     "RP11-20D14.3"  "FMNL1-DT"      "HCG17"        
## [25] "RP11-154H23.4" "AC003099.2"   
## [1] "found 13 genes."

## [1] 30
##  [1] "ST6GAL1"  "FRMD4A"   "SFMBT2"   "DENND1A"  "CHSY1"    "DENND4C" 
##  [7] "TLR2"     "SSBP2"    "ARHGAP18" "JAK1"     "RBM47"    "AXL"     
## [13] "TANC2"    "TLR5"    
## [1] "found 14 genes."

## [1] 31
##  [1] "PLPP1"      "CARMIL1"    "NME3"       "PLGRKT"     "TMEM156"   
##  [6] "MMS22L"     "TMEM144"    "FILIP1L"    "SRGAP3"     "LINC01356" 
## [11] "PTCHD4"     "ST3GAL1"    "PDE8A"      "PILRA"      "RGS1"      
## [16] "GRK3"       "SRGN"       "SEC14L1"    "TMEM65"     "ROBO1"     
## [21] "CYRIA"      "MIR181A1HG" "IFITM10"   
## [1] "found 21 genes."

## [1] 32
##  [1] "TTC7A"         "HAMP"          "PIGL"          "BTG2"         
##  [5] "LIPC"          "MACROD2"       "TTTY14"        "DLEU7"        
##  [9] "LINC02649"     "AC007879.5"    "RP11-202G18.1" "CCDC26"       
## [13] "RFX3-AS1"      "LINC00884"     "RNF217-AS1"    "RP11-360F5.1" 
## [17] "LINC02762"     "CTC-575N7.1"   "RP11-624C23.1" "RP11-463D19.1"
## [21] "SMIM35"        "RP11-196H14.2" "RP11-323I15.5" "COPG2IT1"     
## [1] "found 8 genes."

## [1] 33
##  [1] "KIF26B"   "ADAM22"   "PDE4A"    "CELF4"    "MOB3B"    "TGFBI"   
##  [7] "PPFIA2"   "CACNA1B"  "ARID5B"   "CACNA1C"  "CACNA2D1" "FMN2"    
## [13] "SORCS3"   "SYN2"     "GRM5"     "GRIN1"    "CADM1"    "SYN3"    
## [19] "MYT1L"    "DPYD"     "RYR2"    
## [1] "found 21 genes."

## [1] 34
##  [1] "CALCR"         "MBNL3"         "ADGRG6"        "PID1"         
##  [5] "NMNAT3"        "BEAN1"         "TMC7"          "LINC00476"    
##  [9] "ARSJ"          "SCOC-AS1"      "AC105760.2"    "ZRANB2-AS2"   
## [13] "RP5-1198O20.4" "ITGA9-AS1"     "RP11-634B7.4"  "RORA-AS1"     
## [17] "MIR3142HG"     "LINC00506"     "RP11-622I12.1" "RP11-1H15.4"  
## [21] "RP11-6G22.1"   "MAMLD1"        "SPOCK2"        "TBC1D10C"     
## [25] "LINC01435"     "RP1-179N16.6"  "AGBL1"        
## [1] "found 12 genes."

## [1] 35
##  [1] "CHD5"          "OLFM1"         "CEMIP2"        "CBLN2"        
##  [5] "CDH18"         "CNTN5"         "NPAS3"         "ME3"          
##  [9] "AK5"           "PALM2AKAP2"    "CLSTN2"        "ABCG1"        
## [13] "CAMK2N1"       "LRFN5"         "NEGR1"         "RESF1"        
## [17] "H1-10"         "LSAMP"         "PTPRT"         "CACNA1E"      
## [21] "TOX"           "FAM155A"       "MEG3"          "RP11-191L9.4" 
## [25] "MIAT"          "SHISA9"        "RP11-17A1.3"   "RP11-259O2.1" 
## [29] "RP11-111A21.1"
## [1] "found 22 genes."

## [1] 36
##  [1] "ATP8B1"        "IL7"           "SSPN"          "SHOC1"        
##  [5] "PLD4"          "AC002463.3"    "HNRNPA1P48"    "AC105461.1"   
##  [9] "RP11-142M10.2" "ARHGAP15-AS1"  "RP5-1132H15.1" "LANCL1-AS1"   
## [13] "RP11-575L7.8"  "FBXO30-DT"     "CPB2-AS1"      "RP1-117O3.2"  
## [17] "KDM4A-AS1"     "BCL2L1-AS1"    "RP11-544A12.4" "LRIG2-DT"     
## [21] "RP11-775D22.3" "RHOQ-AS1"      "RP11-506H20.1" "LMO7-AS1"     
## [25] "RP11-66H6.3"   "RP11-126O1.4"  "RP1-256G22.2"  "RP11-261A24.1"
## [29] "RP11-168F24.3" "RP11-13J12.3" 
## [1] "found 5 genes."

## [1] 37
##  [1] "XKR6"      "SKA2"      "KIAA0825"  "KATNAL1"   "PRKAG2"    "CLIP4"    
##  [7] "MXI1"      "PATJ"      "CLVS2"     "ST18"      "PITPNC1"   "RASA2"    
## [13] "ZFYVE28"   "EDIL3"     "DLGAP1"    "JAKMIP2"   "SAMD12"    "CSMD1"    
## [19] "OPCML"     "RALYL"     "KCNIP4"    "SLIT1"     "KAZN"      "BASP1-AS1"
## [25] "SATB1-AS1"
## [1] "found 23 genes."

## [1] 38
##  [1] "ABCB4"         "OMD"           "ACKR4"         "ADAMTS17"     
##  [5] "ABCA8"         "GLT1D1"        "FOLR2"         "MT1E"         
##  [9] "RAB37"         "MCMDC2"        "RP11-131L23.1" "EDNRB-AS1"    
## [13] "SMCR5"         "AC073115.7"    "AC092431.3"    "KIF5C-AS1"    
## [17] "AC073115.6"    "RP5-1101C3.1"  "CTB-161M19.4"  "MTRNR2L8"     
## [21] "RP11-867G2.8"  "PRANCR"        "PSMD7-DT"      "TCF4-AS1"     
## [25] "RP11-121C2.3"  "RP11-413N10.3" "RP11-275G7.2"  "RP11-4F5.3"   
## [29] "GADD45B"      
## [1] "found 12 genes."

## [1] 39
##  [1] "NEXMIF"        "CRYM"          "LRRC6"         "CALY"         
##  [5] "DUOX1"         "HERC6"         "RNF180"        "DOK6"         
##  [9] "TSBP1-AS1"     "RP13-188A5.1"  "PCDH9-AS2"     "IPO9-AS1"     
## [13] "RAP2C-AS1"     "RP11-123B3.2"  "RP11-120A1.1"  "RP11-541P9.3" 
## [17] "ZNF10"         "RP11-493L12.4" "LINC02316"     "CEROX1"       
## [21] "ZNF528-AS1"    "LINC02666"     "RP11-314L11.1" "RP1-80B9.4"   
## [25] "RP4-545L17.11" "RP11-320L2.1"  "RP11-617F9.2"  "LINC01762"    
## [29] "SAP30-DT"     
## [1] "found 8 genes."

## [1] 40
##  [1] "ZNF804B"      "SYT7"         "ADGRL1"       "IGSF9B"       "NALCN"       
##  [6] "KCNT1"        "ARFGEF3"      "DNAH6"        "CSMD2"        "ATP8A1"      
## [11] "PCSK2"        "GPNMB"        "ZNF365"       "BTBD11"       "ZNF385D"     
## [16] "SPOCK1"       "FBXO32"       "GABRB1"       "PRICKLE2"     "ARHGEF3"     
## [21] "ADGRV1"       "SRRM3"        "TMTC2"        "GPC5"         "KCTD16"      
## [26] "RORB"         "CTC-340A15.2" "LINC01414"    "CTC-535M15.2"
## [1] "found 25 genes."

Session information

gc()

##           used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells 4165351 222.5   10243768 547.1         NA 10243768 547.1
## Vcells 8928651  68.2   29538339 225.4      65536 29518146 225.3

sessionInfo()

## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] stringr_1.5.0     limma_3.54.2      tidyr_1.3.0       ggpubr_0.6.0     
## [5] ggplot2_3.4.2     data.table_1.14.8
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.10            png_0.1-8              Biostrings_2.66.0     
##  [4] digest_0.6.31          utf8_1.2.3             R6_2.5.1              
##  [7] GenomeInfoDb_1.34.9    backports_1.4.1        stats4_4.2.3          
## [10] RSQLite_2.3.1          evaluate_0.20          httr_1.4.6            
## [13] pillar_1.9.0           zlibbioc_1.44.0        rlang_1.1.0           
## [16] rstudioapi_0.14        car_3.1-2              jquerylib_0.1.4       
## [19] blob_1.2.4             R.oo_1.25.0            R.utils_2.12.2        
## [22] S4Vectors_0.36.2       rmarkdown_2.21         labeling_0.4.2        
## [25] RCurl_1.98-1.12        bit_4.0.5              munsell_0.5.0         
## [28] broom_1.0.4            compiler_4.2.3         xfun_0.39             
## [31] pkgconfig_2.0.3        BiocGenerics_0.44.0    htmltools_0.5.5       
## [34] tidyselect_1.2.0       KEGGREST_1.38.0        GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1           IRanges_2.32.0         fansi_1.0.4           
## [40] crayon_1.5.2           dplyr_1.1.2            withr_2.5.0           
## [43] R.methodsS3_1.8.2      bitops_1.0-7           grid_4.2.3            
## [46] jsonlite_1.8.4         gtable_0.3.3           lifecycle_1.0.3       
## [49] DBI_1.1.3              magrittr_2.0.3         scales_1.2.1          
## [52] cli_3.6.1              stringi_1.7.12         cachem_1.0.7          
## [55] carData_3.0-5          farver_2.1.1           XVector_0.38.0        
## [58] ggsignif_0.6.4         bslib_0.4.2            generics_0.1.3        
## [61] vctrs_0.6.2            RColorBrewer_1.1-3     org.Hs.eg.db_3.16.0   
## [64] tools_4.2.3            bit64_4.0.5            Biobase_2.58.0        
## [67] glue_1.6.2             purrr_1.0.1            abind_1.4-5           
## [70] fastmap_1.1.1          yaml_2.3.7             AnnotationDbi_1.60.2  
## [73] colorspace_2.1-0       rstatix_0.7.2          memoise_2.0.1         
## [76] knitr_1.44             sass_0.4.5